Chimeric alignment with minimap2
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3.9 years ago

Hi,

On minimap2 github (https://github.com/lh3/minimap2) it says :

For long RNA-seq reads, minimap2 may produce chimeric alignments potentially caused by gene fusions/structural variations or by an intron longer than the max intron length -G (200k by default). For now, it is not recommended to apply an excessively large -G as this slows down minimap2 and sometimes leads to false alignments.

How can I extract such chimeric reads ? Are these only cis-fusions (on the same chromosome) or also trans fusions (different chromosomes) ? Is there a way to tune the chimeric detection ?

Thanks

minimap2 nanopore chimeric • 2.6k views
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Entering edit mode
3.9 years ago
Macspider ★ 3.4k

If the output is a SAM-formatted file, you can retrieve them by including only reads that carry the 0x800 flag, using samtools view -f 0x800.

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